High-throughput and high-accuracy single-cell RNA isoform analysis using PacBio circular consensus sequencing.

Although long-read single-cell RNA isoform sequencing (scISO-Seq) can reveal alternative RNA splicing in individual cells, it suffers from a low read throughput. Here, we introduce HIT-scISOseq, a method that removes most artifact cDNAs and concatenates multiple cDNAs for PacBio circular consensus sequencing (CCS) to achieve high-throughput and high-accuracy single-cell RNA isoform sequencing. HIT-scISOseq can yield >10 million high-accuracy long-reads in a single PacBio Sequel II SMRT Cell 8M. We also report the development of scISA-Tools that demultiplex HIT-scISOseq concatenated reads into single-cell cDNA reads with >99.99% accuracy and specificity. We apply HIT-scISOseq to characterize the transcriptomes of 3375 corneal limbus cells and reveal cell-type-specific isoform expression in them. HIT-scISOseq is a high-throughput, high-accuracy, technically accessible method and it can accelerate the burgeoning field of long-read single-cell transcriptomics.

Angiogenic and Antiangiogenic mechanisms of high density lipoprotein from healthy subjects and coronary artery diseases patients.

Normal high-density lipoprotein (nHDL) in normal, healthy subjects is able to promote angiogenesis, but the mechanism remains incompletely understood. HDL from patients with coronary artery disease may undergo a variety of oxidative modifications, rendering it dysfunctional; whether the angiogenic effect is mitigated by such dysfunctional HDL (dHDL) is unknown. We hypothesized that dHDL compromises angiogenesis. The angiogenic effects of nHDL and dHDL were assessed using endothelial cell culture, endothelial sprouts from cardiac tissue from C57BL/6 mice, zebrafish model for vascular growth and a model of impaired vascular growth in hypercholesterolemic low-density lipoprotein receptor null(LDLr-/-)mice. MiRNA microarray and proteomic analyses were used to determine the mechanisms. Lipid hydroperoxides were greater in dHDL than in nHDL. While nHDL stimulated angiogenesis, dHDL attenuated these responses. Protein and miRNA profiles in endothelial cells differed between nHDL and dHDL treatments. Moreover, nHDL suppressed miR-24-3p expression to increase vinculin expression resulting in nitric oxide (NO) production, whereas dHDL delivered miR-24-3p to inhibit vinculin expression leading to superoxide anion (O2•-) generation via scavenger receptor class B type 1. Vinculin was required for endothelial nitric oxide synthase (eNOS) expression and activation and modulated the PI3K/AKT/eNOS and ERK1/2 signaling pathways to regulate nHDL- and VEGF-induced angiogenesis. Vinculin overexpression or miR-24-3p inhibition reversed dHDL-impaired angiogenesis. The expressions of vinculin and eNOS and angiogenesis were decreased, but the expression of miR-24-3p and lipid hydroperoxides in HDL were increased in the ischemic lower limbs of hypercholesterolemic LDLr-/- mice. Overexpression of vinculin or miR-24-3p antagomir restored the impaired-angiogenesis in ischemic hypercholesterolemic LDLr-/- mice. Collectively, nHDL stimulated vinculin and eNOS expression to increase NO production by suppressing miR-24-3p to induce angiogenesis, whereas dHDL inhibited vinculin and eNOS expression to enhance O2•- generation by delivering miR-24-3p to impair angiogenesis, and that vinculin and miR-24-3p may be therapeutic targets for dHDL-impaired angiogenesis.

Protein Compositions Changes of Circulating Microparticles in Patients With Valvular Heart Disease Subjected to Cardiac Surgery Contribute to Systemic Inflammatory Response and Disorder of Coagulation.

We recently demonstrated that circulating microparticles (MPs) from patients with valvular heart diseases (VHD) subjected to cardiac surgery impaired endothelial function and vasodilation. However, it is unknown whether or not the protein composition of these circulating MPs actually changes in response to the disease and the surgery. Circulating MPs were isolated from age-matched control subjects (n = 50) and patients (n = 50) with VHD before and 72 h after cardiac surgery. Proteomics study was performed by liquid chromatography and mass spectrometry combined with isobaric tags for relative and absolute quantification technique. The differential proteins were identified by ProteinPilot, some of which were validated by Western blotting. Bio-informatic analysis of differential proteins was carried out. A total of 849 proteins were identified and 453 proteins were found in all three groups. Meanwhile, 165, 39, and 80 proteins were unique in the control, pre-operation, and postoperation groups respectively. The unique proteins were different in localization, molecular function, and biological process. The pro-inflammatory proteins were increased in VHD patients and more so postoperatively. Proteins related to coagulation were dramatically changed before and after surgery. The protein composition of circulating MPs was changed in patients with VHD undergoing cardiac surgery, which may lead to activation of the systemic inflammatory response and disorders of coagulation.

[Proteomic analysis between keloid and normal skin].

OBJECTIVE: To investigate and search correlative proteins of keloid by comparing the results of differential proteomic analysis between keloid and normal skin. METHODS: From January 2010 to June 2010 two-dimensional gel electrophoresis was used to define patterns of protein expression in keloid skin from 8 patients and matched normal skin from 3 patients. Differential expression protein spots were showed and analyzed by matrix-assisted laser desorption ionization-time of flying/time of flying (MALDI-TOF/TOF) mass spectrometry. RESULTS: This study succeeded to provide a two-dimensional protein profiling comparison between normal skin and keloid. Gel-analysis software identified an average of 2978 spots in keloid while 3053 spots in normal skin and statistical filtering yielded 40 spots of a 4-fold change, 32 of which were identified by using mass spectrometry, 20 were up-regulated and 12 were down-regulated. Functional analysis revealed that these proteins could be fractionated to carrier proteins (3 proteins), signal transduction proteins (4 proteins), proliferation and apoptosis related proteins (2 proteins), cytoskeleton proteins (6 proteins), extracellular matrix proteins (8 proteins), immunity related proteins (3 proteins), tumor related proteins (2 proteins), and function unknown protein (4 proteins). CONCLUSIONS: Proteomic analysis can identify the proteins with variance of keloid versus normal skin. The further research to these differential proteins may help reveal the pathogenesis of keloid and provide new treatments for keloid.

Identification of cancer-associated proteins by proteomics and downregulation of ß-tropomyosin expression in colorectal adenoma and cancer.

Elucidating the molecular mechanism underlying the development of adenoma, the major precursor lesion of colorectal cancer (CRC), would provide a basis for early detection, prevention as well as treatment of CRC. Using the highly sensitive 2-D DIGE method coupled with MS, we identified 24 differentially expressed proteins in adenoma tissues compared with matched normal colonic mucosa and CRC tissues. Fifteen proteins were downregulated and three proteins were upregulated in adenoma tissues when compared with individual-matched normal colonic mucosa. Five proteins were downregulated, while one protein was upregulated in adenoma tissues when compared with matched CRC tissues. A protein, ß-tropomyosin (TM-ß), recently suggested to be a biomarker of esophageal squamous carcinoma, was downregulated in both adenoma and CRC tissues. Additionally, the reduction in the level of TM-ß in adenoma and CRC tissues was further validated by Western blotting (p<0.05) and RT-PCR (p<0.001). Our findings suggest that downregulation of TM-ß is involved in the early development of CRC and that differentially expressed proteins might serve as potential biomarkers for detection of CRC.